A 1100-year long record of lake ecosystem response to climate and catchment change with precise chronological control is reported. Diatom and pollen assemblages of an annually laminated (varved) sediment from a northern Swedish lake (Kassjön, Våsterbotten) were used as records of lake diatom communities and catchment vegetation. These data were compared with summer temperature estimates based on tree-ring records of the same geographical area to identify the effects of climate change and catchment disturbance on diatom assemblages in the lake. In a canonical ordination, 23% of the variability in the total diatom assemblages for the period AD1040–1804 was accounted for by changes in pollen data which reflect agricultural development in the catchment. Diatom species richness, however, exhibited a stronger relationship with summer temperature and, significantly, declined with the lower temperatures associated with the Little Ice Age minimum (early 17th century). Summer temperature accounted for 23% of the variability in diatom species richness 20 years later. The mechanism behind this time-lag is unclear, but may be related to catchment-mediated effects, given recent evidence for lags in the response of boreal-forest vegetation regeneration cycles to climatic variability. These results suggest that climate-related effects on lakes occurring over medium timescales can be resolved in lake sediments. Moreover, it is possible to identify these effects despite cultural-related signals, but as the latter become more extreme in the late 20th century the climate signal is obscured.